Genetic diversity analysis of Chinese plum (Prunus salicina L.) based on whole-genome resequencing

Abstract

Chinese plum (Prunus salicina L.), also known as Japanese plum, is gaining importance because of its extensive genetic diversity and nutritional attributes that are beneficial for human health. Single-nucleotide polymorphisms (SNPs) are the most abundant form of genomic polymorphisms and are widely used in population genetics research. In this study, we constructed high-quality SNPs through whole-genome resequencing of 67 Prunus accessions with a depth of ~20× to evaluate the genome-level diversity and population structure. Phylogenetic analysis, principal component analysis, and population structure profiling indicated that the 67 plum accessions could be classified into four groups corresponding to their origin location, the southern cultivar group (SCG), the northern cultivar group (NCG), the foreign cultivar group (FG), and the mixed cultivar group (MG). Some cultivars from South China clustered with the other three groups. The genetic diversity indices including private allele number, observed heterozygosity, expected heterozygosity, and the nucleotide diversity of the SCG were higher than those of the NCG. Gene flow from the SCG to FG was also detected. Based on the distribution of wild resources, we concluded that the domestication center of origin of the Chinese plum was southwestern China. This study also provided genetic variation features and the population structure of Chinese plum cultivars, laying a foundation for breeders to use diverse germplasm and allelic variants to improve Chinese plum varieties.

Chromosome‐scale genome assembly and population genomics provide insights into the adaptation, domestication, and flavonoid metabolism of Chinese plum

“…We examined the relationships and divergence among the different ecological populations of the 78 Prunus accessions (Table S1). Using the high-depth (approximately 209) whole-genome re-sequencing data of these accessions generated in our study (22 of the 78) and reported by others (56 of the 78) (Jiang et al, 2019;Wei et al, 2021), we identified 13 548 616 single nucleotide polymorphisms (SNPs) and 1 090 237 small insertion/deletions (InDels). After imputation and filtering, we obtained 3 380 659 highquality SNPs for further analysis; the average SNP frequency was nearly one per 100 bp (Figure S13).…”

“…Southwest China was previously assumed to be a primitive domestication center of Chinese plum, which was evidenced by the discovery of wild plum communities in the middle reaches of the Yangtze River Basin (Hartmann and Neumulle, 2009;Wei et al, 2020;Zhang and Zhou, 1998), a palynology investigation (Guo, 2006), a large-scale phenotypic variation analysis (Yu et al, 2011), and multiple genetic diversity analyses (Chen and Yang, 2014;Wei et al, 2019Wei et al, , 2021Zuo et al, 2015). The results of the present study were consistent with those findings.…”

“…Of the 78 Prunus accessions used in our study, the raw reads of P. armeniaca were obtained from the China National GeneBank Sequence Archive (CNSA) (https://db.cngb.org/cnsa/) with enquiry number CNP0000755 (Jiang et al, 2019). The raw reads of the other 55 Prunus accessions were obtained from the Sequence Read Archive of the NCBI (https://www.ncbi.nlm.nih.gov/sra/) with enquiry number PRJNA659814 (Wei et al, 2021). Whole-genome re-sequencing of the remaining 22 accessions was conducted in the current study at high coverage (approximately 209) using the Illumina HiSeq X-ten platform (Illumina) with the PE150 sequencing strategy (Table S1).…”

“…A palynological study showed that the P. salicina in South China is more primitive than that in North China (Guo, 2006). The genetic diversity of Chinese plums cultivated in Southwest China was higher than that of Chinese plums in Northern China using a large-scale phenotypic variation analysis (Yu et al, 2011) and molecular tests with multiple types of markers (Chen and Yang, 2014;Wei et al, 2019Wei et al, , 2021Zuo et al, 2015), which was in accordance with the fact that there were wild plum populations discovered in Yunnan, Sichuan, and Guizhou Provinces (Wei et al, 2020;Zhang and Zhou, 1998). It is speculated that plums were introduced to Japan by a Chinese monk of high standing who brought the trees as a gift to the Emperor; alternatively, a naturalized Japanese, Wani, might also have brought plums to Japan from the Korean peninsula (Faust and Suranyi, 1999).…”

An Upgraded, Highly Saturated Linkage Map of Japanese Plum (Prunus salicina Lindl.), and Identification of a New Major Locus Controlling the Flavan-3-ol Composition in Fruits

“…The Japanese plum (Prunus salicina Lindl.) is a self-incompatible, diploid (2n = 16) species, originated in China, that produces an edible drupe (Topp et al, 2012;Wei et al, 2021). Also, it is known to be a rich source of phenolic compounds, whose types of molecules and their contents vary greatly among cultivars (Rothwell et al, 2013;Venter et al, 2014;Roussos et al, 2016).…”